GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Pantoea rwandensis LMG 26275

Align Galactose-proton symporter; Galactose transporter (characterized)
to candidate WP_084936573.1 HA51_RS21365 sugar porter family MFS transporter

Query= SwissProt::P0AEP1
         (464 letters)



>NCBI__GCF_002095475.1:WP_084936573.1
          Length = 464

 Score =  764 bits (1972), Expect = 0.0
 Identities = 386/462 (83%), Positives = 421/462 (91%), Gaps = 1/462 (0%)

Query: 1   MPDAKKQGR-SNKAMTFFVCFLAALAGLLFGLDIGVIAGALPFIADEFQITSHTQEWVVS 59
           MP    + R SNK MT FVCFLAALAGLLFGLDIGVIAGALPFIA +F +T+H QEW+VS
Sbjct: 1   MPGTTHKSRTSNKMMTLFVCFLAALAGLLFGLDIGVIAGALPFIAKDFNVTAHQQEWIVS 60

Query: 60  SMMFGAAVGAVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLILSRVLLGLAV 119
           SMMFGAAVGAVGSGW+S +LGRKKSLM GAILFV GSL+SA A + ++LI +RV+LGLAV
Sbjct: 61  SMMFGAAVGAVGSGWMSSRLGRKKSLMAGAILFVIGSLWSAMATSPDMLIAARVVLGLAV 120

Query: 120 GVASYTAPLYLSEIAPEKIRGSMISMYQLMITIGILGAYLSDTAFSYTGAWRWMLGVIII 179
           GVASYTAPLYLSEIAPEKIRGSMIS+YQLMITIGIL AYLSDTAFS  GAWRWMLGVI I
Sbjct: 121 GVASYTAPLYLSEIAPEKIRGSMISLYQLMITIGILAAYLSDTAFSDAGAWRWMLGVITI 180

Query: 180 PAILLLIGVFFLPDSPRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIRESLQVKQSGW 239
           PAILLLIGVFFLP+SPRW AAK  F  A+RVL RLRDTS +AKRELDEIRESL++KQSGW
Sbjct: 181 PAILLLIGVFFLPNSPRWLAAKGDFRSAQRVLDRLRDTSEQAKRELDEIRESLKIKQSGW 240

Query: 240 ALFKENSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYTNTTEQMWGTVIVGLT 299
            LF+ NS+FRRAV+LGVLLQVMQQFTGMNVIMYYAPKIFE+AG+ NTT+QMWGTVIVGL 
Sbjct: 241 QLFQSNSHFRRAVYLGVLLQVMQQFTGMNVIMYYAPKIFEIAGFANTTQQMWGTVIVGLV 300

Query: 300 NVLATFIAIGLVDRWGRKPTLTLGFLVMAAGMGVLGTMMHIGIHSPSAQYFAIAMLLMFI 359
           NVLATFIAIGLVDRWGRKPTL LGF+VMAAGMG+LGTM+HIGIHS SAQYFA+AMLLMFI
Sbjct: 301 NVLATFIAIGLVDRWGRKPTLVLGFIVMAAGMGILGTMLHIGIHSASAQYFAVAMLLMFI 360

Query: 360 VGFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLNTLGNANTFW 419
           VGFAMSAGPLIWVLCSEIQPLKGRDFGIT STATNWIANMIVGATFLTMLN+LGNA TFW
Sbjct: 361 VGFAMSAGPLIWVLCSEIQPLKGRDFGITVSTATNWIANMIVGATFLTMLNSLGNAPTFW 420

Query: 420 VYAALNVLFILLTLWLVPETKHVSLEHIERNLMKGRKLREIG 461
           VYA LNV FILLT+ L+PETK+VSLEHIERNLM G+KLR+IG
Sbjct: 421 VYAGLNVFFILLTVALIPETKNVSLEHIERNLMSGKKLRDIG 462


Lambda     K      H
   0.327    0.140    0.425 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 914
Number of extensions: 32
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 464
Length of database: 464
Length adjustment: 33
Effective length of query: 431
Effective length of database: 431
Effective search space:   185761
Effective search space used:   185761
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory